What do you mean "can't reflash the BIOS". What stops you?
Describe "Windows won't load up fully." Specifics - do you get an error message? Does it just reboot? Does it just hang? Does it BSOD?
What output do you get when you
boot in verbose mode?
Have you tried a new SATA/IDE cable? Have you tried a new SATA/IDE port (you should have several)? Are the drives on the same channel?
Also - how clean is your clean installation?